org.jmol.adapter.readers.more
Class GhemicalMMReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.GhemicalMMReader

public class GhemicalMMReader
extends AtomSetCollectionReader

Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files. !Header mm1gp 100 !Info 1 !Atoms 6 0 6 1 6 2 1 3 1 4 1 5 1 !Bonds 5 1 0 D 2 0 S 3 0 S 4 1 S 5 1 S !Coord 0 0.06677 -0.00197151 4.968e-07 1 -0.0667699 0.00197154 -5.19252e-07 2 0.118917 -0.097636 2.03406e-06 3 0.124471 0.0904495 -4.84021e-07 4 -0.118917 0.0976359 -2.04017e-06 5 -0.124471 -0.0904493 5.12591e-07 !Charges 0 -0.2 1 -0.2 2 0.1 3 0.1 4 0.1 5 0.1 !End

Author:
Egon Willighagen

Field Summary
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup
 
Constructor Summary
GhemicalMMReader()
           
 
Method Summary
(package private)  void processAtoms()
           
(package private)  void processBonds()
           
(package private)  void processCharges()
           
(package private)  void processCoord()
           
(package private)  void processHeader()
           
(package private)  void processInfo()
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GhemicalMMReader

public GhemicalMMReader()
Method Detail

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class AtomSetCollectionReader

processHeader

void processHeader()

processInfo

void processInfo()

processAtoms

void processAtoms()
            throws java.lang.Exception
Throws:
java.lang.Exception

processBonds

void processBonds()
            throws java.lang.Exception
Throws:
java.lang.Exception

processCoord

void processCoord()
            throws java.lang.Exception
Throws:
java.lang.Exception

processCharges

void processCharges()
              throws java.lang.Exception
Throws:
java.lang.Exception